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Onions are the large, round life forms that act as nests for the Pikmin. There are three known types of Onion nests, each with unique coloration corresponding to either Red, Yellow, or Blue Pikmin, and only one of each has ever been seen. As of Pikmin 2, subterranean species such as Purple Pikmin, White Pikmin and Bulbmin do not have Onions.
In Pikmin 3, all discovered onions merge together the night after they are discovered, and become a single, universal Onion, greatly simplifying the management of Pikmin types at the beginning of each day.
Onions require light, as in Pikmin 3, the Yellow Onion did not activate until a nearby light source was turned on, even when approached.
It also appears that the Onions in Pikmin 3 are much more malleable than their Pikmin and Pikmin 2 counterparts in regards to which Pikmin species they will hold. In Pikmin 3, you discover a new Onion color and leave that new color of Pikmin at your landing site instead of at their home Onion, the Master Onion at the landing site will accommodate them until the Onion Fusion at the end of the day.